Hello,
  I am new to selection test, apologize if this is a very lame question. I used MEME to detect positive selection but found it hard to report the result, despite reading through the reference you suggest for MEME. I am wondering in the result table, besides p value, what’s worth to report (α, β¯ and β+) since other tests (etc FEL) would give you a clear dS and dN value to report in a common scientific way. Any suggestion??

Thanks in advance,

Yun

Dear Yun,

MEME reports a distribution of dN/dS for the site -- this is the key difference (and the key improvement) when MEME is compared to something like FEL. You should emphasize in reporting the results that the method infers more than just the mean dS and dN.

I would report the following for each site that you want to include:

p-value (does the site have evidence of episodic selection)
α -- a measure of synonymous variability
β- / α -- the strength of purifying selection at the site
weight of β- -- what proportion of branches are under purifying selection
β+ / α -- the strength of diversifying selection at the site
weight of β- -- what proportion of branches are under diversifying selection

Sergei

Dear Sergei

This is very helpful!!
Thank you very much :-----------)

Yun